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10.3390/microorganisms12010162
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Article

Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome

by
Adriana Soria-Villalba
1,†,
Nicole Pesantes
2,3,†,
Nuria Jiménez-Hernández
2,3,
Javier Pons
2,
Andrés Moya
2,3,4 and
Vicente Pérez-Brocal
2,3,*
1
Vall d’Hebron Research Institute (VHIR), 08035 Barcelona, Spain
2
Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain
3
Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
4
Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), 46980 Valencia, Spain
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2024, 12(1), 162; https://doi.org/10.3390/microorganisms12010162
Submission received: 21 December 2023 / Revised: 10 January 2024 / Accepted: 11 January 2024 / Published: 13 January 2024
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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Abstract

Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.
Keywords: virome; RNA; VLP; bulk metagenomics; NetoVIR; SISPA; sequencing virome; RNA; VLP; bulk metagenomics; NetoVIR; SISPA; sequencing

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MDPI and ACS Style

Soria-Villalba, A.; Pesantes, N.; Jiménez-Hernández, N.; Pons, J.; Moya, A.; Pérez-Brocal, V. Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms 2024, 12, 162. https://doi.org/10.3390/microorganisms12010162

AMA Style

Soria-Villalba A, Pesantes N, Jiménez-Hernández N, Pons J, Moya A, Pérez-Brocal V. Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms. 2024; 12(1):162. https://doi.org/10.3390/microorganisms12010162

Chicago/Turabian Style

Soria-Villalba, Adriana, Nicole Pesantes, Nuria Jiménez-Hernández, Javier Pons, Andrés Moya, and Vicente Pérez-Brocal. 2024. "Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome" Microorganisms 12, no. 1: 162. https://doi.org/10.3390/microorganisms12010162

APA Style

Soria-Villalba, A., Pesantes, N., Jiménez-Hernández, N., Pons, J., Moya, A., & Pérez-Brocal, V. (2024). Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms, 12(1), 162. https://doi.org/10.3390/microorganisms12010162

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